Re: [PyMOL] colored secondary structure of two chains with different colors [resolved]
Thank you vevry much Annemarie it worked -- Stéphane Abel, Ph.D. Commissariat à l’Energie Atomique et aux Energies Alternatives Centre de Saclay DSV/ISVFJ/SB2SM Bat 528, Office 138C Gif-sur-Yvette, F-91191 FRANCE Phone (portable) : +33 6 49 37 70 60 -- Message: 1 Date: Thu, 6 Jun 2019 12:49:56 +0200 From: ahoneg To: pymol-users@lists.sourceforge.net Subject: [PyMOL] colored secondary structure of two chains with different colors Message-ID: Content-Type: text/plain; charset=utf-8 Dear St?phane, by default, the cartoon representation takes its color from the color of the c-alpha atoms of your protein. However, you can override this default and assign a specific color to the cartoon representation of a given selection by: set cartoon_color, color, (selection) e.g. set cartoon_color, red, resi 1-60 best regards Annemarie Honegger Dr. Annemarie Honegger Dept. of Biochemistry Z?rich University Winterthurerstrasse 190 8057 Z?rich Switzerland e-mail: honeg...@bioc.uzh.ch phone: +41 44 635 55 62 fax:+41 44 635 57 12 > > Message: 4 > Date: Thu, 6 Jun 2019 10:26:29 + > From: ABEL Stephane > To: "h. adam steinberg" > Cc: "pymol-users@lists.sourceforge.net" > > Subject: Re: [PyMOL] colored secondary structure of two chains with > different colors > Message-ID: > <3e39b768bb199548ab18f7289e7534af4b042...@exdag0-b0.intra.cea.fr> > Content-Type: text/plain; charset="Windows-1252" > > Hi Adam > > OK I can colored each chain with different colors. But it is not exactly what > I want. Indeed in the figure* > > - the AA are in sticks with the different colors for each atom --> I can do > this > - the beta sheet in the monomer are in red and blue ---> I can "not" do this > even if I use your suggestion > > I would like in two representations at the same time and the necessary > commands for adding them in a script. > ript. > > *https://cdn.rcsb.org/images/rutgers/ma/1mag/1mag.pdb-500.jpg > > Thank you again. > > St?phane > > > -- > St?phane Abel, Ph.D. > Commissariat ? l?Energie Atomique et aux Energies Alternatives > Centre de Saclay DSV/ISVFJ/SB2SM > Bat 528, Office 138C > Gif-sur-Yvette, F-91191 FRANCE > Phone (portable) : +33 6 49 37 70 60 > ________________ > De : h. adam steinberg [h.adam.steinb...@gmail.com] > Envoy? : mercredi 5 juin 2019 21:36 > ? : ABEL Stephane > Objet : Re: [PyMOL] colored secondary structure of two chains with different > colors > > If you change your mouse / selection mode to chains, you can then click on > one of the monomers and choose a color for it from the (sale) in the right > side panel drop down menu. Then click on the other monomer and do the same. > > Is that what you are asking for? > >> On Jun 5, 2019, at 1:23 PM, ABEL Stephane wrote: >> >> Hello all >> >> I have a pdb structure of gramicidin A dimer (PDB 1MAG) and I would like to >> color the beta sheets of each monomer with different colors (for instance >> in red and blue colors) in Figure >> >> https://cdn.rcsb.org/images/rutgers/ma/1mag/1mag.pdb-500.jpg >> >> How to do this ? >> >> Thank you >> >> St?phane >> >> >> >> ___ >> PyMOL-users mailing list >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> Unsubscribe: >> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > > > > > -- > > > > -- > > Subject: Digest Footer > > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > > -- > > End of PyMOL-users Digest, Vol 157, Issue 5 > *** -- -- Subject: Digest Footer ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- End of PyMOL-users Digest, Vol 157, Issue 6 *** ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] colored secondary structure of two chains with different colors
Dear Stéphane, by default, the cartoon representation takes its color from the color of the c-alpha atoms of your protein. However, you can override this default and assign a specific color to the cartoon representation of a given selection by: set cartoon_color, color, (selection) e.g. set cartoon_color, red, resi 1-60 best regards Annemarie Honegger Dr. Annemarie Honegger Dept. of Biochemistry Zürich University Winterthurerstrasse 190 8057 Zürich Switzerland e-mail: honeg...@bioc.uzh.ch phone: +41 44 635 55 62 fax:+41 44 635 57 12 > > Message: 4 > Date: Thu, 6 Jun 2019 10:26:29 + > From: ABEL Stephane > To: "h. adam steinberg" > Cc: "pymol-users@lists.sourceforge.net" > > Subject: Re: [PyMOL] colored secondary structure of two chains with > different colors > Message-ID: > <3e39b768bb199548ab18f7289e7534af4b042...@exdag0-b0.intra.cea.fr> > Content-Type: text/plain; charset="Windows-1252" > > Hi Adam > > OK I can colored each chain with different colors. But it is not exactly what > I want. Indeed in the figure* > > - the AA are in sticks with the different colors for each atom --> I can do > this > - the beta sheet in the monomer are in red and blue ---> I can "not" do this > even if I use your suggestion > > I would like in two representations at the same time and the necessary > commands for adding them in a script. > ript. > > *https://cdn.rcsb.org/images/rutgers/ma/1mag/1mag.pdb-500.jpg > > Thank you again. > > St?phane > > > -- > St?phane Abel, Ph.D. > Commissariat ? l?Energie Atomique et aux Energies Alternatives > Centre de Saclay DSV/ISVFJ/SB2SM > Bat 528, Office 138C > Gif-sur-Yvette, F-91191 FRANCE > Phone (portable) : +33 6 49 37 70 60 > ________________ > De : h. adam steinberg [h.adam.steinb...@gmail.com] > Envoy? : mercredi 5 juin 2019 21:36 > ? : ABEL Stephane > Objet : Re: [PyMOL] colored secondary structure of two chains with different > colors > > If you change your mouse / selection mode to chains, you can then click on > one of the monomers and choose a color for it from the (sale) in the right > side panel drop down menu. Then click on the other monomer and do the same. > > Is that what you are asking for? > >> On Jun 5, 2019, at 1:23 PM, ABEL Stephane wrote: >> >> Hello all >> >> I have a pdb structure of gramicidin A dimer (PDB 1MAG) and I would like to >> color the beta sheets of each monomer with different colors (for instance >> in red and blue colors) in Figure >> >> https://cdn.rcsb.org/images/rutgers/ma/1mag/1mag.pdb-500.jpg >> >> How to do this ? >> >> Thank you >> >> St?phane >> >> >> >> ___ >> PyMOL-users mailing list >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> Unsubscribe: >> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > > > > > -- > > > > -- > > Subject: Digest Footer > > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > > -- > > End of PyMOL-users Digest, Vol 157, Issue 5 > *** ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] colored secondary structure of two chains with different colors
Hi Adam OK I can colored each chain with different colors. But it is not exactly what I want. Indeed in the figure* - the AA are in sticks with the different colors for each atom --> I can do this - the beta sheet in the monomer are in red and blue ---> I can "not" do this even if I use your suggestion I would like in two representations at the same time and the necessary commands for adding them in a script. ript. *https://cdn.rcsb.org/images/rutgers/ma/1mag/1mag.pdb-500.jpg Thank you again. Stéphane -- Stéphane Abel, Ph.D. Commissariat à l’Energie Atomique et aux Energies Alternatives Centre de Saclay DSV/ISVFJ/SB2SM Bat 528, Office 138C Gif-sur-Yvette, F-91191 FRANCE Phone (portable) : +33 6 49 37 70 60 De : h. adam steinberg [h.adam.steinb...@gmail.com] Envoyé : mercredi 5 juin 2019 21:36 À : ABEL Stephane Objet : Re: [PyMOL] colored secondary structure of two chains with different colors If you change your mouse / selection mode to chains, you can then click on one of the monomers and choose a color for it from the (sale) in the right side panel drop down menu. Then click on the other monomer and do the same. Is that what you are asking for? > On Jun 5, 2019, at 1:23 PM, ABEL Stephane wrote: > > Hello all > > I have a pdb structure of gramicidin A dimer (PDB 1MAG) and I would like to > color the beta sheets of each monomer with different colors (for instance in > red and blue colors) in Figure > > https://cdn.rcsb.org/images/rutgers/ma/1mag/1mag.pdb-500.jpg > > How to do this ? > > Thank you > > Stéphane > > > > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] colored secondary structure of two chains with different colors
Hello all I have a pdb structure of gramicidin A dimer (PDB 1MAG) and I would like to color the beta sheets of each monomer with different colors (for instance in red and blue colors) in Figure https://cdn.rcsb.org/images/rutgers/ma/1mag/1mag.pdb-500.jpg How to do this ? Thank you Stéphane ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
